Recently the getGEO function of the package GEOquery suddenly started throwing the following error:

   gse=getGEO("GSE106977",GSEMatrix=T)

    #https://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106977/matrix/
    #OK
    #Found 2 file(s)
    #/geo/series/GSE106nnn/GSE106977/
    #Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", ; :
    #cannot open destfile 'C:\Users\Marti\AppData\Local\Temp\Rtmp8cEqMH//geo/series/GSE106nnn/GSE106977',    reason 'No such file or directory'

After some debuging I found that there was an error in the getAndParseGSEMatrices hidden function

To overcome this issue I made a patch, that fix the issue.

First copy this code into Rstudio or worpad

    getAndParseGSEMatrices=function (GEO, destdir, AnnotGPL, getGPL = TRUE) 
    {
      GEO <- toupper(GEO)
      stub = gsub("\d{1,3}$", "nnn", GEO, perl = TRUE)
      gdsurl <- "https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/";
      b = getDirListing(sprintf(gdsurl, stub, GEO))
      b=b[-1]
      message(sprintf("Found %d file(s)", length(b)))
      ret <- list()
      for (i in 1:length(b)) {
        message(b[i])
        destfile = file.path(destdir, b[i])
        if (file.exists(destfile)) {
          message(sprintf("Using locally cached version: %s", destfile))
        }
        else {
          download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", ;
                                stub, GEO, b[i]), destfile = destfile, mode = "wb", 
                        method = getOption("download.file.method.GEOquery"))
        }
        ret[[b[i]]] <- parseGSEMatrix(destfile, destdir = destdir, 
                                      AnnotGPL = AnnotGPL, getGPL = getGPL)$eset
      }
      return(ret)
    }
    environment(getAndParseGSEMatrices)<-asNamespace("GEOquery")
    assignInNamespace("getAndParseGSEMatrices", getAndParseGSEMatrices, ns="GEOquery")

Save the file as  GEOpatch.R  in your working directory and

then, when loading the GEOquery library, source the saved file:

    library(GEOquery)
    source("GEOpatch.R")

Now it should get going...

    gse=getGEO("GSE106977",GSEMatrix=T)
    #https://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106977/matrix/
    #OK
    #Found 1 file(s)
    #GSE106977_series_matrix.txt.gz
    #trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106977/matrix/GSE106977_series_matrix.txt.gz';
    #Content type 'application/x-gzip' length 32707196 bytes (31.2 MB)

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] GEOquery_2.40.0      Biobase_2.34.0       BiocGenerics_0.20.0 
[4] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] httr_1.3.1      R6_2.2.2        tools_3.3.2     RCurl_1.95-4.10
[5] bitops_1.0-6    XML_3.98-1.9   
> 

very useful, it worked..!!